- Introduction to metabolomics
- Preprocessing of LC-MS data in Bioconductor
- Normalization
- Annotation/identification
12 July 2018
Sample is dissolved in a fluid (mobile phase).
Mobile phase carries analytes through a column with a stationary phase.
Sample is dissolved in a fluid (mobile phase).
Mobile phase carries analytes through a column with a stationary phase.
Separation based on affinity for the column’s stationary phase.
Sample is dissolved in a fluid (mobile phase).
Mobile phase carries analytes through a column with a stationary phase.
Separation based on affinity for the column’s stationary phase.
HILIC (hyrophilic liquid interaction chromatography):
Hydrophilic, polar stationary phase.
Analytes solved in mobile phase.
Analytes separated by polarity: low polarity elute first, high polarity later.
LC-MS data has thus 3 dimensions:
Analyze the data along retention time.
readMSData (MSnbase package):xcms: findChromPeaks function, passing settings along with an algorithm-specific parameter object.cwp <- CentWaveParam(peakwidth = c(2, 10), snthresh = 5) data <- findChromPeaks(data, param = cwp) head(chromPeaks(data), n = 3)
## mz mzmin mzmax rt rtmin rtmax into intb ## CP001 114.0907 114.0899 114.0929 1.954 0.280 3.907 1559.829 1555.923 ## CP002 114.0913 114.0884 114.0929 5.860 4.465 8.650 1890.221 1885.757 ## CP003 114.0914 114.0899 114.0929 10.882 8.650 13.114 1950.953 1946.210 ## maxo sn sample is_filled ## CP001 584.9510 584 1 0 ## CP002 601.8881 601 1 0 ## CP003 691.9580 691 1 0
xcms: adjustRtime function with PeakDensityParam [Smith et al. Anal. chem. 2006] or ObiwarpParam [Prince et al. Anal. chem. 2006].xcms: groupChromPeaks with NearestPeaksParam [Katajamaa et al. Bioinformatics 2006] and PeakDensityParam [Smith et al. Anal. chem. 2006].xcms: groupChromPeaks with NearestPeaksParam [Katajamaa et al. Bioinformatics 2006] and PeakDensityParam [Smith et al. Anal. chem. 2006].
peak density approach (for a given m/z slice):
## DataFrame with 4 rows and 4 columns ## mzmed rtmed POOL_1 POOL_2 ## <numeric> <numeric> <numeric> <numeric> ## FT001 105.041814839707 167.961095453642 229.490739260736 3093.75184315684 ## FT002 105.041653033614 157.083057856508 4762.39872227772 6601.45091358641 ## FT003 105.069636149683 31.8108067962868 699.723986763235 1033.23232267732 ## FT004 105.11027064078 63.7513630255991 20211.2633706294 15839.5504368189
Match compounds based on features’ m/z.
Will result in an 1:n mapping.
Identify compounds based on m/z and:
CompoundDb package (similar to ensembldb and alike): contains compound data + spectra.MSnbase).xcms.